Biology subjects

Kelly, D.

Publications and source records attributed to Kelly, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatiotemporal bioprinting of microtissues and growth factors within a support bath to engineer anisotropic, zonally defined meniscal grafts

Current clinical treatments for meniscal injuries remain limited and are associated with an increased risk of developing osteoarthritis (OA). This has motivated the development of tissue engineering (TE) strategies to engineer more biomimetic meniscal grafts capable of promoting functional joint regeneration. Existing approaches typically fail to recapitulate the zonal heterogeneity of the native meniscus, which contains distinct inner and outer regions with unique extracellular matrix (ECM) composition and organization. Here, we introduce a novel bioprinting strategy using spatially patterned growth factors and mesenchymal stromal/stem cell (MSC)-derived microtissues ({micro}Ts) to engineer meniscal constructs with zonally defined structure and composition. We first investigated the effects of different growth factor regimes, specifically connective tissue growth factor (CTGF) and transforming growth factor-{beta}3 (TGF-{beta}3), on fibrochondrogenesis of MSC-derived {micro}Ts. While TGF-{beta}3 alone promoted a more inner-zone meniscus phenotype, stimulation of {micro}Ts with a combination of TGF-{beta}3 and CTGF supported the development of tissues that more closely mimicked the outer zone of the meniscus. Using laponite to control the release of these growth factors, it was also possible to bioprint zonally defined meniscal tissue within a methacrylate xanthan gum (XG-MA) support bath. A fibro-ink containing {micro}Ts, CTGF and TGF-{beta}3 supported higher collagen type I deposition and lower collagen type II deposition, while a chondro-ink containing {micro}Ts and TGF-{beta}3 promoted higher collagen type II deposition. Based on these findings, dual-cartridge bioprinting was next used to spatially pattern {micro}Ts with CTGF + TGF-{beta}3 (fibro-ink) or TGF-{beta}3 (chondro-ink) to generate regionally defined, meniscal-like engineered tissues. This approach enabled the bioprinting of scaffold-free constructs with aligned collagen and zone-specific ECM depositions, with an inner region consisting of sGAG and collagen types I and II, and an outer region rich in sGAG and collagen type I. These findings highlight the potential of co-printing both growth factors and MSC-derived {micro}Ts for engineering scaffold-free, zonally defined meniscal tissues.

bioengineering↗

bioRxiv2026

AE-PocketMiner Uses Attention to Simultaneously Predict Cryptic Pockets and Their Allosteric Coupling

Finding and targeting cryptic pockets could dramatically expand the druggable proteome. However, discovering these sites remains challenging since they are only open a fraction of the time. It is also difficult to predict the functional relevance of a cryptic site as this often requires insight into allostery. Here we introduce attention enabled (AE-)PocketMiner, an artificial intelligence (AI) method that uses a graph neural network with an attention mechanism to simultaneously predict the locations of cryptic pockets and their allosteric coupling to the rest of the protein from a single input structure. We show that AE-PocketMiner outperforms past methods for identifying cryptic pockets and recapitulates known allosteric interactions. Moreover, we experimentally confirm newly predicted cryptic pockets and mutations that allosterically control pocket opening. AE-PocketMiner thus provides a powerful framework for multiple steps of the drug discovery process--including pocket identification, prioritization, and assay design--that will help expand the druggable proteome.

biophysics↗

bioRxiv2026

Molecular adaptations of activated T-cells in an inflammation-associated schizophrenia sub-group

Thirty-five percent of people with schizophrenia-related disorders (SRD) form a high-inflammation subgroup defined by elevated anti-gliadin antibodies (AGA+) and inflammatory proteins and associated with an increased severity of negative symptoms. However, the immune mechanisms mediating these effects remain poorly defined. Here, we characterized transcriptional signatures of peripheral immune cells in AGA+ SRD (n=7) compared to AGA-negative (AGA-) SRD (n=3) and healthy controls (HC; n=5), using single-cell RNA-sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs). AGA+ SRD was associated with increased abundance of T-helper-17 cells (Th17), T-follicular helper-1 (Tfh1), CD5+ B cells, plasmacytoid dendritic cells (pDCs), and several CD8+ T cell subsets, including memory and Natural Killer-T-like activated subsets. In parallel, AGA-SRD exhibited a higher abundance of several monocyte subsets compared to either AGA+ SRD or HC. Pathway analysis revealed upregulation in AGA+ SRD of JAK/STAT, type I Interferon, and IL-6 signaling pathways in distinct subset of activated T-cells. Collectively, these results define a unique T cell predominant inflammatory signature in AGA+ SRD, as well as potential targets for therapeutic intervention.

genomics↗

bioRxiv2026

Ruminosignatures associated with methane emissions and feed efficiency across geographies and cattle breeds

The cattle rumen microbiota represents a highly complex and dynamic ecosystem, whose organization and connection to host phenotypes are of the highest importance to food security and the environment. In this study, we analyzed the rumen microbiota, from 2,492 cattle belonging to five different breeds and production systems across five countries, categorizing them into microbial co-abundance groups referred to as Ruminosignatures. We identified twelve distinct Ruminosignatures, including two that were consistently observed across all populations and were dominated by the genus Prevotella and UBA2810. Additional Ruminosignatures showed breed-and diet-specific patterns and collectively explained 96-99% of the variance in rumen microbial composition. The abundances of several Ruminosignatures were associated with methane emissions and feed efficiency, and were influenced by host genetics, with heritability estimates ranging from 0.09 to 0.51. The Ruminosignature dominated by UAB2810 was negatively associated with methane emissions across all datasets and positively linked to feed efficiency in Holstein from Italy and crossbred from Ireland. Additionally, the type of production system affects both the occurrence of Ruminosignatures and their impact on host phenotypes, emphasizing the need for context-specific approaches to modulate the rumen microbiome. Overall, our results offer new perspectives on the assembly of ruminal microbes and underscore the potential of the Ruminosignatures framework for microbiome-informed precision agriculture and breeding initiatives aimed at enhancing feed efficiency and minimizing the environmental impact of cattle farming.

microbiology↗

bioRxiv2026

Dityrosine photocrosslinking of native collagen bioinks for controlled shape-fidelity of bioprinted cardiac tissue constructs: probing the interplay between fibrillogenesis and covalent bond formation

Collagen bioinks are widely used in biofabrication, but their relatively soft mechanical properties can lead to structural instabilities under cell-generated contraction forces. While synthetic functional groups can be conjugated for covalent crosslinking, these methods often disrupt natural protein fibrillogenesis, thereby compromising collagen fibre architecture. This work presents a strategy for the direct covalent stabilisation of native collagen bioinks with dityrosine bonds via visible-light photocrosslinking with ruthenium (Ru) and sodium persulfate (SPS), avoiding the need for polymer pre-functionalisation. Multimodal characterisation, including high-resolution microscopy, spectroscopy, mass spectrometry, and nanoindentation, identified photocrosslinking conditions that enhance collagen fibrillogenesis and reduce off-target polymer oxidation. Interestingly, the biofabrication process itself affected ultimate collagen fibre architecture, with shear-induced alignment during extrusion enhancing fibril proximity and self-assembly, overcoming inhibitory effects the crosslinkers had on fibrillogenesis via ionic and electrostatic interactions. Leveraging these insights, embedded bioprinting was used to fabricate cardiac constructs with high cell viability (>80%), where dityrosine crosslinking could be tuned to modulate geometric shape changes under cell-generated forces (1-15% shrinkage). Finally, the platform was used to bioprint anatomically accurate double-ventricle human heart models with robust shape fidelity. This research establishes a versatile photocrosslinking framework for bioprinting cardiac constructs with tunable shape stability using native collagen bioinks.

bioengineering↗

bioRxiv2026

Developmentally inspired bioprinting of nascent multicellular human heart tissue through in situ differentiation and morphogenesis of iPSCs

Traditional heart tissue bioprinting typically relies on using human induced pluripotent stem cell (iPSC)-derived cardiomyocytes that are pre-differentiated in 2D culture. This approach differs fundamentally from embryonic heart development, where mesodermal progenitors differentiate into cardiomyocytes within 3D, matrix-rich, and shape-morphing microenvironments. Here, we introduce a novel developmentally inspired approach that enables in situ mesodermal and cardiac differentiation of iPSCs within bioprinted, shape-morphing pluripotent tissues. Using embedded bioprinting, Matrigel bioinks with high-density iPSC suspensions were deposited into granular support hydrogels to generate pluripotent tissue constructs with defined architectures. These constructs exhibited shape-morphing behaviour, tunable by modulating the support bath viscoelasticity. Support bath mechanics also regulated iPSC fate, with softer formulations reducing spontaneous differentiation. Building on this, mesodermal induction and cardiogenesis were directly driven within the morphing constructs via temporal WNT pathway modulation, resulting in multicellular cardiac tissues in which cardiomyocytes, fibroblasts, and endothelial cells co-emerge from a common progenitor pool. Importantly, these nascent tissues underwent structural maturation, with immunofluorescence and gene expression profiling revealing cardiac progenitors alongside maturing cardiomyocytes. Together, these findings highlight the potential for a new paradigm in biofabrication focused on printing pluripotent organ rudiments that recapitulate key aspects of embryonic development and support progressive tissue maturation.

bioengineering↗

bioRxiv2025

Tetramerisation governs SALL transcription factor function in development and disease

Spalt-like (SALL) proteins are C2H2 zinc-finger transcription factors important for embryogenesis, with mutations in SALL1 and SALL4 causing rare congenital disorders Townes-Brocks and Okihiro syndromes, respectively. While SALL proteins are known to associate with one another, the biological significance of the resulting complexes is unknown. Here we define a conserved glutamine-rich region that mediates SALL1/4 homo- and heterotetramerisation and find that complex formation is indispensable for DNA binding. Modelling a patient mutation that abolishes SALL4 multimerisation led to gene misregulation and, in mice, embryonic lethality, therefore phenocopying a complete Sall4 knockout. Furthermore, a common disease-causing SALL1 truncation, which retains multimerisation but lacks DNA-binding domains, sequesters SALL4 into heterotetramers that are defective in DNA binding, thereby providing a mechanistic explanation for the dominant-negative effects of many Townes-Brocks mutations. Together, our findings establish tetramerisation as a prerequisite for SALL function, linking complex formation to developmental gene regulation and human disease.

molecular biology↗

bioRxiv2025

A 4D Bioprinting Platform to Engineer Anisotropic Musculoskeletal Tissues by Spatially Patterning Microtissues into Temporally Adapting Support Baths

Bioprinting is a powerful tool for engineering living tissues, however replicating native composition, structure and function remains a major challenge. During morphogenesis, cellular self-organization and matrix development are strongly influenced by the mechanical constraints provided by surrounding tissues, suggesting that such biophysical cues should be integrated into bioprinting strategies to engineer more biomimetic grafts. Here we introduce a novel 4D bioprinting platform that spatially patterns mesenchymal stem/stromal cell (MSC)-derived microtissues into temporally adapting support baths. By modulating the baths mechanical properties, we can precisely control the physical constraints applied post-printing, directing both filament geometry and cellular behavior. Support bath stiffness regulated mechano-sensitive gene expression and microtissue phenotype, with softer matrices favoring chondrogenesis and stiffer environments promoting (myo)fibrogenic differentiation. In addition, the physical properties of the support bath modulated microtissue fusion and extracellular matrix organization, with increased collagen fiber alignment in stiffer baths. Leveraging these findings, it was possible to engineer either articular cartilage, meniscus, or ligament grafts with user defined collagen architectures by simply varying the physical properties of the support bath. This platform establishes a foundation for bioprinting structurally anisotropic and phenotypically distinct constructs, thereby enabling the scalable engineering of a range of different musculoskeletal tissues.

bioengineering↗

bioRxiv2024

Autonomous control of extrusion bioprinting using convolutional neural networks

Extrusion bioprinting technology suffers from reproducibility challenges due to the open-loop nature of current hardware systems. Here, we present a novel AI-powered extrusion bioprinting platform with integrated real-time quality monitoring and automated error correction capabilities. To achieve this, we engineered a custom bioprinting system with an integrated camera for continuous process monitoring and trained convolutional neural networks (CNNs) to classify the extrusion process in real-time. The CNN models, including Xception and ResNet, were trained on a combination of real and synthetic data to classify extrusion quality (good, over, or under) across various printing scenarios, including single-line and infill patterns. Notably, transfer learning, utilizing synthetic data for initial training followed by refinement with real-world data enhanced classification accuracy, with the Xception model displaying 90% accuracy for single-line extrusion and 75% for infill extrusion. This intelligent monitoring system was then coupled with a closed-loop control system that dynamically adjusted extrusion parameters on-the-fly to correct errors. The platform successfully corrected both over- and under-extrusion errors for alginate and collagen bioinks with varying rheological properties, demonstrating adaptability to unseen materials. Importantly, extrusion errors were corrected within [~]10 seconds. This novel closed-loop bioprinting platform represents a significant advance over traditional open-loop systems.

bioengineering↗

bioRxiv2024

A functional screen uncovers circular RNAs regulating excitatory synaptogenesis in hippocampal neurons

Circular RNAs (circRNAs) are an expanding class of largely unexplored RNAs which are prominently enriched in the mammalian brain. Here, we systematically interrogated their role in excitatory synaptogenesis of rat hippocampal neurons using RNA interference. Thereby, we identified seven circRNAs as negative regulators of excitatory synapse formation, many of which contain high-affinity microRNA binding sites. Knockdown of one of these candidates, circRERE, surprisingly promoted the formation of electrophysiologically silent synapses. Mechanistically, circRERE knockdown resulted in a preferential upregulation of synaptic mRNAs containing binding sites for miR-128-3p because of a reduced protective interaction between miR-128-3p and circRERE. Accordingly, overexpression of circRERE rescued exaggerated synapse formation upon circRERE knockdown in a miR-128-3p binding site-specific manner. Overall, our results uncover circRERE-mediated stabilization of miR-128-3p as a novel mechanism to restrict the formation of silent excitatory synaptic co-clusters and more generally implicate circRNA-dependent microRNA regulation in the control of synapse development and function.

neuroscience↗

bioRxiv2024

Leaf abaxial and adaxial surfaces differentially affect plant-fungal pathogen interactions

Eudicot plant species have bifacial leaves with each surface varying in a diversity of components, resulting in potentially different microhabitats for pathogens. We tested how Botrytis cinerea, a necrotroph fungal pathogen, interacts with the two different leaf surfaces across 16 crop species and 20 Arabidopsis genotypes. This showed that the abaxial surface is generally more susceptible to the pathogen than the adaxial surface. In Arabidopsis, the differential lesion area between leaf surfaces was associated to jasmonic acid (JA) and salicylic acid (SA) signaling and differential induction of defense chemistry. When infecting the adaxial surface, leaves mounted stronger defenses by producing more glucosinolates and camalexin defense compounds, partially explaining the differential susceptibility across surfaces. Testing a collection of 96 B. cinerea strains showed genetic heterogeneity of growth patterns, with a few strains preferring the adaxial surface while most are more virulent on the abaxial surface. Overall, we show that leaf-Botrytis interactions are complex with host-specific, surface-specific, and strain-specific behaviors. Within Arabidopsis, this mechanistically links to potential variation in JA/SA signaling across the two surfaces.

plant biology↗

bioRxiv2023

Melt electrowritten scaffold architectures to mimic vasculature mechanics and control neo-tissue orientation

Cardiovascular disease is one of the leading causes of death worldwide, commonly associated with the development of an arteriosclerotic plaque and impairment of blood flow in arteries. Current adopted grafts to bypass the stenosed vessel fail to recapitulate the unique mechanical behaviour of native vessels, particularly in the case of small diameter vessels (<6 mm), leading to graft failure. Therefore, in this study, melt-electrowriting (MEW) was adopted to produce a range of fibrous grafts to mimic the extracellular matrix (ECM) architecture of the tunica media of vessels, in an attempt to match the mechanical and biological behaviour of the native tissue. Initially, the range of collagen architectures within the native vessel was determined, and subsequently replicated using MEW (winding angles (WA) 45{degrees}, 26.5{degrees}, 18.4{degrees}, 11.3{degrees}). These scaffolds recapitulated the anisotropic, non-linear mechanical behaviour of native carotid blood vessels. Moreover, these grafts facilitated human mesenchymal stromal/stem cell (hMSC) infiltration, differentiation, and ECM deposition that was independent of WA. The bioinspired MEW fibre architecture promoted cell alignment and preferential neo-tissue orientation in a manner similar to that seen in native tissue, particularly for WA 18.4{degrees} and 11.3{degrees}, which is a mandatory requirement for long-term survival of the regenerated tissue post-scaffold degradation. Lastly, the WA 18.4{degrees} was translated to a tubular graft and was shown to mirror the mechanical behaviour of small diameter vessels within physiological strain. Taken together, this study demonstrates the capacity to use MEW to fabricate bioinspired grafts to mimic the tunica media of vessels and recapitulate vascular mechanics which could act as a framework for small diameter graft development and functional long-term tissue regeneration.

bioengineering↗

bioRxiv2022

Localized nanoparticle-mediated delivery of miR-29b normalises the dysregulation of bone homeostasis caused by osteosarcoma whilst simultaneously inhibiting tumour growth.

Patients diagnosed with osteosarcoma undergo extensive surgical intervention and chemotherapy resulting in dismal prognosis and compromised quality of life owing to poor bone regeneration, which is further compromised with chemotherapy delivery. This study aims to investigate if localised delivery of miR-29b--which has been shown to promote bone formation by inducing osteoblast differentiation and also to suppress prostate and glioblastoma tumour growth--would suppress osteosarcoma tumours whilst simultaneously normalising the dysregulation of bone homeostasis caused by osteosarcoma. Thus, we studied the therapeutic potential of miR-29b to promote bone remodelling in an orthotopic model of osteosarcoma (rather than in bone defect models using healthy mice), and in the context of chemotherapy, that is clinically relevant. We developed a formulation of miR-29b:nanoparticles that were delivered via a novel hyaluronic-based hydrogel to enable local and sustained release of the therapy, and to study the potential of attenuating tumour growth whilst normalising bone homeostasis. We found that when miR-29b was delivered along with systemic chemotherapy, compared to chemotherapy alone, our therapy provided a significant decrease in tumour burden, increase in mouse survival, and a significant decrease in osteolysis thereby normalising the dysregulation of bone lysis activity caused by the tumour.

bioengineering↗

bioRxiv2021

Metabolic and Proteomic Defects in Human Hypertrophic Cardiomyopathy

RationaleImpaired cardiac energetics in hypertrophic cardiomyopathy (HCM) is thought to result from increased ATP utilization at the sarcomere and is believed to be central to pathophysiology. However, the precise defects in cardiac metabolism and substrate availability in human HCM have not been defined. ObjectiveThe purpose of this study is to define major disease pathways and determine the pool sizes of intermediary metabolites in human HCM. Methods and ResultsWe conducted paired proteomic and metabolomic analyses of septal myectomy samples from patients with HCM and compared results to non-failing control human hearts. Increased abundance of extracellular matrix and intermediate filament / Z-disc proteins, and decreased abundance of proteins involved in fatty acid oxidation and cardiac energetics was evident in HCM compared to controls. Acyl carnitines, byproducts of fatty acid oxidation, were markedly depleted in HCM samples. Conversely, the ketone body 3-hydroxybutyrate, lactate, and the 3 branched chain amino acids, were all significantly increased in HCM hearts, suggesting that they may serve as alternate fuel sources for the production of ATP. ATP, nicotinamide adenine dinucleotide (NADH), NADP and NADPH, and acetyl CoA were also severely depleted in HCM hearts. Based on measurements from human skinned muscle fibers, the magnitude of observed reduction in ATP content in the HCM hearts would be expected to decrease the rate of cross-bridge detachment, implying a direct effect of energy depletion on myofilament function that could contribute to diastolic dysfunction. ConclusionsHCM hearts display profound deficits in cardiac energetics, marked by depletion of fatty acid derivatives and compensatory increases in other metabolites that could serve as alternate fuel sources. These results lend support to the paradigm that energy depletion contributes to the pathophysiology of HCM and also have important therapeutic implications for the future design of metabolic modulators to treat HCM.

physiology↗

bioRxiv2021

RNA pull-down-Confocal Nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-Synuclein levels

RNA-protein interactions are central to all gene expression processes and contribute to variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as incurable. Here we developed a fluorescent on-bead screening platform: RNA pull-down-Confocal Nanoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7s primary target is an mRNA of -Synuclein, which contributes to aetiology of Parkinsons disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of -Synuclein. This opens up new therapeutic avenues towards treatment of Parkinsons disease as well as provides novel methodology to search for RNA-protein interaction modulators.

molecular biology↗

bioRxiv2020

STING Nuclear Partners Contribute to Innate Immune Signalling Responses

STING and cGAS initiate innate immune responses (IIR) by recognizing cytoplasmic pathogen dsDNA and activating signaling cascades from the ER; however, another less investigated pool of STING resides in the nuclear envelope. We find that STING in the inner nuclear membrane increases mobility and changes localization upon IIR activation both from dsDNA and poly(I:C) stimuli. We next identified nuclear partners of STING from isolated nuclear envelopes. These include several known nuclear membrane proteins, bromodomain and epigenetic enzymes, and RNA- or DNA-binding proteins. Strikingly, 17 of these DNA and RNA-binding STING partners are known to bind direct partners of the IRF3/7 transcription factors that are central drivers of IIR. We find that several of these STING partners --SYNCRIP, Men1, Ddx5, snRNP70, RPS27a, Aatf-- can contribute to IIR activation and SYNCRIP can moreover protect against influenza A virus infection. These data suggest that the many roles identified for STING likely reflect its interactions with multiple RNA and DNA-binding proteins that also function in IIR.

immunology↗

bioRxiv2020

Connexin 43 confers chemoresistance through activating PI3K

Circumventing chemoresistance is crucial for effectively treating glioblastoma due to limited therapeutic options. The gap junction protein connexin 43 (Cx43) renders glioblastoma resistant to the frontline chemotherapy temozolomide; however, targeting Cx43 is difficult because mechanisms underlying Cx43-mediated chemoresistance remain elusive. Here we show that Cx43, but not other connexins, is highly expressed in glioblastoma and strongly correlates with poor patient prognosis and chemoresistance, making Cx43 the prime therapeutic target among all connexins. The intracellular carboxyl terminus of Cx43 binds to phosphatidylinositol 3-kinase (PI3K) catalytic subunit {beta} (PIK3CB, also called PI3K{beta} or p110{beta}), thereby activating PI3K signaling independent of Cx43-channels and subsequently inducing temozolomide resistance. A combination of CT1, a Cx43-targeting peptide inhibitor, and PIK3CB-selective inhibitors restores temozolomide sensitivity in vitro and in vivo. This study not only reveals novel mechanistic insights into chemoresistance in glioblastoma, but also demonstrates that targeting Cx43 and PIK3CB/p110{beta} is an effective approach for overcoming chemoresistance.

cancer biology↗

bioRxiv2020

Neuronal non-CG methylation is an essential target for MeCP2 function

SUMMARYDNA methylation is implicated in neuronal biology via the protein MeCP2, mutation of which causes Rett syndrome. MeCP2 recruits the NCOR1/2 corepressor complexes to methylated cytosine in the CG dinucleotide, but also to non-CG methylation, which is abundant specifically in neuronal genomes. To test the biological significance of its dual binding specificity, we replaced the MeCP2 DNA binding domain with an orthologous domain whose specificity is restricted to mCG motifs. Knock-in mice expressing the domain-swap protein displayed severe Rett syndrome-like phenotypes, demonstrating that interaction with sites of non-CG methylation, specifically the mCAC trinucleotide, is critical for normal brain function. The results support the notion that the delayed onset of Rett syndrome is due to the late accumulation of both mCAC and its reader MeCP2. Intriguingly, genes dysregulated in both Mecp2-null and domain-swap mice are implicated in other neurological disorders, potentially highlighting targets of particular relevance to the Rett syndrome phenotype.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗